First the mistrust. According to NPR, American officials acknowledge that the Pakistan Army had made significant gains in fighting the Taliban in Bajaur but still wanted them to do more to stop militants crossing over into Kunar. “Elements of the Taliban and al-Qaida are believed to cross the border at this point from safe havens inside Pakistan.”

The two conflicting views give an interesting insight into how the narrative of mistrust in Kunar and Bajaur – a microcosm of the strains in the wider U.S.-Pakistan relationship — is constructed. In particular, you can see how distrust between Pakistanis and Americans is magnified by the mutual suspicion of Afghans and Pakistanis.

Look at this detail in the NPR story, presented under a bold-type sub-heading reading “Taliban in Their Midst?”

The Americans are invited to lunch by the Pakistanis. “The long lunch ends when the Pakistani colonel is called away, and the Americans walk back up the hill. Full bellies, heavy flak jackets, and the altitude at 7,000 feet have everyone moving a bit slowly, but then they get some information from their interpreter that makes them walk a little faster. The interpreter tells the soldiers that some of the Pakistani commander’s men are spies for the Taliban. ‘So he suggests we get out of here quickly,’ a soldier tells (Captain Thomas) Billig,” the NPR reports.

Whatever goodwill might have been generated by the lunch is presumably undone by the words of the Afghan interpreter, whose warning about alleged Pakistani duplicity appears to have been taken at face value. You see similar accusations against Afghans in the Pakistani media, where they are accused of helping militants in Kunar to attack Pakistan.

We are never going to be in a position to know for sure what is going on. What we should be able to do, however, especially nine years into the war in Afghanistan, is to understand better why soldiers on either side of the Pakistan-Afghan border think the way they do.

Second, is the CIA base on the border.

The NPR says interviews with Pakistani border guards and U.S. soldiers, and some Pakistani press reports, all suggest that the CIA built this massive base compound more than two years ago. “The construction included a road, the helicopter landing zone and several hard structures, including one at the top of the mountain called ‘Camp Karzai’.”

The base at the Ghakhi Pass served to keep the border under control while U.S. soldiers were fighting in a valley to the west. It was recently evacuated, in what NPR quotes a U.S. intelligence official as describing as ”an orderly closure of a U.S. government facility that involved coordination with the U.S. military.”

Yet neither the American nor the Pakistani soldiers in the area appeared to have had any warning. “”Why didn’t you tell us they were pulling out?” the Pakistani colonel asks Captain Billig over lunch, adding that his border guards would have adjusted if they knew the other side was suddenly going to be empty. “Billig simply nods in agreement, and allows that the abrupt departure came as a surprise to him as well,” NPR says.

I can’t find anything to explain why the base was set up two years ago, nor why it was abandoned now — unless it was part of U.S. plans to pull back from remote areas and concentrate on counter-insurgency in populated areas.

But compare its operations with what was going on in Bajaur in the same time period.

Bajaur was long believed to be a base for top al Qaeda leaders - Osama bin Laden’s deputy Ayman al-Zawahiri was repeatedly rumoured to be hiding there some years back — and it was the target for some of the earliest drone strikes. Was the CIA base linked to the hunt for al Qaeda? And does the closure of the base mean al Qaeda has moved elsewhere?

Two years ago, militants had all but overrun Bajaur, setting up a parallel administration and raining rockets down on the army base in the town of Khar. It got so bad that the army feared even the fort at Khar might be overrun. After 20 months of intense fighting, in which 150 Pakistani soldiers died and 637 were injured, the Pakistan Army managed to clear out most of the main militant strongholds in Bajaur, and have since been taking foreign journalists on organised trips to show what they had achieved.

Yet even when we were there back in April, we were told the gains from the military offensive would gradually fall away unless a civilian administration could be brought in to restore governance in the region, and compensation paid to those whose homes had been destroyed in the fighting. I have not seen any evidence that has happened – the civilian administration, never good at the best of times, has been stretched beyond the limit in trying to cope with the devastating floods which hit Pakistan this summer.

So you would assume the security situation in Bajaur may well be deteriorating — an assumption supported by this Jamestown Foundation round-up of press reports on Bajaur released in August, which says it is a emerging as a new hub of Islamist militancy. Why would you therefore choose now, of all times, to abandon a base which was meant to limit movement across the border?

It is pretty difficult to get answers to these questions. What you can say is there seems to be a fairly serious problem with coordination on the ground on either side of the Pakistan-Afghan border. And that in turn creates more and more distrust, poisoning relations between Pakistan and the United States right up the chain of command until you reach the so-far unsuccessful attempt to create a strategic partnership between the two.

(Reuters photo: Abandoned caves used by militants in Bajaur/Adrees Latif)